Nasonia vitripennis vs Apis mellifera LastZ Results

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Nasonia vitripennis (Nasonia vitripennis, Nvit_2.1) and Apis mellifera (Apis mellifera, Amel_4.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Nasonia vitripennis was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 63,753

Genome coverage (bp) Coding exon coverage (bp)
Nasonia vitripennis

Uncovered: 271,930,299 out of 295,780,872
Covered: 23,850,573 out of 295,780,872

Uncovered: 11,483,855 out of 24,175,229
Matches: 8,441,438 out of 24,175,229
Mismatches: 3,907,643 out of 24,175,229
Insertions: 342,293 out of 24,175,229

Apis mellifera

Uncovered: 226,915,363 out of 250,270,657
Covered: 23,355,294 out of 250,270,657

Uncovered: 5,487,360 out of 19,369,619
Matches: 9,342,026 out of 19,369,619
Mismatches: 4,250,535 out of 19,369,619
Insertions: 289,698 out of 19,369,619

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Nasonia vitripennis Apis mellifera
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}